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He P, Zhang X, Xia K, Green DE, Baytas S, Xu Y, Pham T, Liu J, Zhang F, Almond A, Linhardt RJ, DeAngelis PL. Chemoenzymatic synthesis of sulfur-linked sugar polymers as heparanase inhibitors. Nat Commun 2022; 13:7438. [PMID: 36460670 PMCID: PMC9718760 DOI: 10.1038/s41467-022-34788-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Complex carbohydrates (glycans) are major players in all organisms due to their structural, energy, and communication roles. This last essential role involves interacting and/or signaling through a plethora of glycan-binding proteins. The design and synthesis of glycans as potential drug candidates that selectively alter or perturb metabolic processes is challenging. Here we describe the first reported sulfur-linked polysaccharides with potentially altered conformational state(s) that are recalcitrant to digestion by heparanase, an enzyme important in human health and disease. An artificial sugar donor with a sulfhydryl functionality is synthesized and enzymatically incorporated into polysaccharide chains utilizing heparosan synthase. Used alone, this donor adds a single thio-sugar onto the termini of nascent chains. Surprisingly, in chain co-polymerization reactions with a second donor, this thiol-terminated heparosan also serves as an acceptor to form an unnatural thio-glycosidic bond ('S-link') between sugar residues in place of a natural 'O-linked' bond. S-linked heparan sulfate analogs are not cleaved by human heparanase. Furthermore, the analogs act as competitive inhibitors with > ~200-fold higher potency than expected; as a rationale, molecular dynamic simulations suggest that the S-link polymer conformations mimic aspects of the transition state. Our analogs form the basis for future cancer therapeutics and modulators of protein/sugar interactions.
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Affiliation(s)
- Peng He
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY, 12180, USA
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Wenyuan Road 1, Nanjing, 210023, China
| | - Ke Xia
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY, 12180, USA
| | - Dixy E Green
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma, OK, 73104, USA
| | - Sultan Baytas
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY, 12180, USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Truong Pham
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY, 12180, USA
| | - Andrew Almond
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1, 7DN, United Kingdom
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY, 12180, USA.
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma, OK, 73104, USA.
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Eastman J, Allen D, Mumma K, Almond A, Theiling J. Point-of-Care Laboratory Data Collection During Critical Care Transport. Air Med J 2020; 40:81-83. [PMID: 33455635 DOI: 10.1016/j.amj.2020.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/22/2020] [Accepted: 09/19/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Critical care transport involves a high level of intensive clinical care in a resource-limited environment. These patients require multiple assessments guiding specialty treatments, including blood product administration, intravenous electrolyte replacement, ventilator management, and extracorporeal membrane oxygenation. This study aims to measure the usage of point-of-care (POC) laboratory data during critical care transport. METHODS Data were collected via electronic medical record review over 1 year of use in a hospital-based critical care rotor wing, fixed wing, and ground critical care transport team in the Southeastern United States. RESULTS One hundred twenty POC tests were performed during 1,075 critical care transports over the 1-year period (8.9%). Patient transportations involved 35 extracorporeal membrane oxygenation, 21 medical, 17 cardiac, 13 neonatal, 11 respiratory failure, 8 gastrointestinal bleeding, 6 neurologic, 5 pediatrics, 3 trauma, and 1 organ donor. Seventy-eight POC laboratory tests (65%) required intervention, including ventilator changes (39.7%), electrolyte replacement (35.8%), blood products (7.6%), and other (12.8%). The remaining 42 (35%) POC laboratory tests confirmed no intervention was necessary (n = 35) and that ongoing treatments were effective (n = 7). CONCLUSION POC laboratory testing performed during critical care transport guides providers in performing essential emergent interventions in a timelier manner that may benefit critically ill patients.
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Affiliation(s)
- Jamie Eastman
- Duke University Hospital, Durham, NC; Vermont Army National Guard, Medical Detachment, Colchester, VT.
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Wilson AL, Outeiral C, Dowd SE, Doig AJ, Popelier PLA, Waltho JP, Almond A. Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides. Commun Chem 2020; 3:56. [PMID: 36703475 PMCID: PMC9814580 DOI: 10.1038/s42004-020-0298-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 04/06/2020] [Indexed: 01/29/2023] Open
Abstract
Ribonucleic acids (RNAs) are key to the central dogma of molecular biology. While Raman spectroscopy holds great potential for studying RNA conformational dynamics, current computational Raman prediction and assignment methods are limited in terms of system size and inclusion of conformational exchange. Here, a framework is presented that predicts Raman spectra using mixtures of sub-spectra corresponding to major conformers calculated using classical and ab initio molecular dynamics. Experimental optimization allowed purines and pyrimidines to be characterized as predominantly syn and anti, respectively, and ribose into exchange between equivalent south and north populations. These measurements are in excellent agreement with Raman spectroscopy of ribonucleosides, and previous experimental and computational results. This framework provides a measure of ribonucleoside solution populations and conformational exchange in RNA subunits. It complements other experimental techniques and could be extended to other molecules, such as proteins and carbohydrates, enabling biological insights and providing a new analytical tool.
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Affiliation(s)
- Alex L. Wilson
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Carlos Outeiral
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Sarah E. Dowd
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Andrew J. Doig
- grid.5379.80000000121662407Division of Neuroscience and Experimental Psychology, Michael Smith Building, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PT Manchester, UK
| | - Paul L. A. Popelier
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Jonathan P. Waltho
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK ,grid.11835.3e0000 0004 1936 9262Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN Sheffield, UK
| | - Andrew Almond
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
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4
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Lane RS, Haller FM, Chavaroche AAE, Almond A, DeAngelis PL. Heparosan-coated liposomes for drug delivery. Glycobiology 2018; 27:1062-1074. [PMID: 29044377 DOI: 10.1093/glycob/cwx070] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/03/2017] [Indexed: 11/13/2022] Open
Abstract
Liposomal encapsulation is a useful drug delivery strategy for small molecules, especially chemotherapeutic agents such as doxorubicin. Doxil® is a doxorubicin-containing liposome ("dox-liposome") that passively targets drug to tumors while reducing side effects caused by free drug permeating and poisoning healthy tissues. Polyethylene glycol (PEG) is the hydrophilic coating of Doxil® that protects the formulation from triggering the mononuclear phagocyte system (MPS). Evading the MPS prolongs dox-liposome circulation time thus increasing drug deposition at the tumor site. However, multiple doses of Doxil® sometimes activate an anti-PEG immune response that enhances liposome clearance from circulation and causes hypersensitivity, further limiting its effectiveness against disease. These side effects constrain the utility of PEG-coated liposomes in certain populations, justifying the need for investigation into alternative coatings that could improve drug delivery for better patient quality of life and outcome. We hypothesized that heparosan (HEP; [-4-GlcA-β1-4-GlcNAc-α1-]n) may serve as a PEG alternative for coating liposomes. HEP is a natural precursor to heparin biosynthesis in mammals. Also, bacteria expressing an HEP extracellular capsule during infection escape detection and are recognized as "self," not a foreign threat. By analogy, coating drug-carrying liposomes with HEP should camouflage the delivery vehicle from the MPS, extending circulation time and potentially avoiding immune-mediated clearance. In this study, we characterize the postmodification insertion of HEP-lipids into liposomes by dynamic light scattering and coarse-grain computer modeling, test HEP-lipid immunogenicity in rats, and compare the efficacy of drug delivered by HEP-coated liposomes to PEG-coated liposomes in a human breast cancer xenograft mouse model.
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Affiliation(s)
- Rachel S Lane
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA
| | - F Michael Haller
- Caisson Biotech, LLC, 655 Research Park, Oklahoma City, OK 73104, USA
| | | | - Andrew Almond
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA.,Caisson Biotech, LLC, 655 Research Park, Oklahoma City, OK 73104, USA
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5
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Jing W, Roberts JW, Green DE, Almond A, DeAngelis PL. Synthesis and characterization of heparosan-granulocyte-colony stimulating factor conjugates: a natural sugar-based drug delivery system to treat neutropenia. Glycobiology 2018; 27:1052-1061. [PMID: 28973394 DOI: 10.1093/glycob/cwx072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/05/2017] [Indexed: 11/14/2022] Open
Abstract
Many injectable drugs require delivery strategies for enhancing their pharmacokinetics due to rapid loss via renal filtration if possess low molecular weight (<60-70 kDa) and/or clearance by the body's components (e.g., proteases, antibodies, high-efficiency receptors) in their native form. FDA-approved polyethylene glycol (PEG) is a vehicle for improving therapeutics, but artificial polymers have potential biocompatibility and immunogenicity liabilities. Here, we utilized a natural vertebrate carbohydrate, heparosan (HEP), the biosynthetic precursor of heparan sulfate and heparin, to enhance performance of a biologic drug. The HEP polysaccharide was stable with a long half-life (~8 days for 99-kDa chain) in the nonhuman primate bloodstream, but was efficiently degraded to very short oligosaccharides when internalized by cells, and then excreted into urine and feces. Several HEP-modified human granulocyte-colony stimulating factor (G-CSF) conjugates were synthesized with defined quasi-monodisperse HEP polysaccharide chains. Single dosing of 55- or 99-kDa HEP-G-CSF in rats increased blood neutrophil levels comparable to PEG-G-CSF conjugates. Repeated dosing of HEP-G-CSF or HEP alone for 2 weeks did not cause HEP-specific toxic effects in rats. HEP did not possess the anticoagulant behavior of its daughter, heparin, based on testing in rats or clinical diagnostic assays with human plasma. Neither anti-HEP IgG nor IgM antibodies were detected in a long-term (9 doses over 7 months) immunogenicity study of the HEP-drug conjugate with rats. These proof-of-concept experiments with HEP-G-CSF indicate that it is a valid drug candidate for neutropenia and suggest the potential of this HEP-based platform as a safe alternative delivery vehicle for other therapeutics.
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Affiliation(s)
- Wei Jing
- Caisson Biotech, LLC, 655 Research Parkway, Suite 525, Oklahoma City, OK 73104, USA
| | - Jonathan W Roberts
- Caisson Biotech, LLC, 655 Research Parkway, Suite 525, Oklahoma City, OK 73104, USA
| | - Dixy E Green
- University of Oklahoma Health Sciences Center, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA
| | - Andrew Almond
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Paul L DeAngelis
- University of Oklahoma Health Sciences Center, Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA
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6
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Almond A. Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges. Curr Opin Struct Biol 2017; 50:58-64. [PMID: 29253714 DOI: 10.1016/j.sbi.2017.11.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Accepted: 11/26/2017] [Indexed: 01/24/2023]
Abstract
Glycosaminoglycans are long unbranched and complex polysaccharides that are an essential component of mammalian extracellular matrices. Characterization of their molecular structure, dynamics and interactions are essential to understand important biological phenomena in health and disease, and will lead to novel therapeutics and medical devices. However, this has proven to be a challenge experimentally and theoretical techniques are needed to develop new hypotheses, and interpret experiments. This review aims to examine the current theoretical (rather than experimental) methods used by researchers to investigate glycosaminoglycan structure, dynamics and interactions, from the monosaccharide to the macromolecular scale. It will consider techniques such as quantum mechanics, molecular mechanics, molecular dynamics, coarse graining and docking.
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Affiliation(s)
- Andrew Almond
- School of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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7
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Abstract
Proteoglycan spatiotemporal organization underpins extracellular matrix biology, but atomic scale glimpses of this microarchitecture are obscured by glycosaminoglycan size and complexity. To overcome this, multimicrosecond aqueous simulations of chondroitin and dermatan sulfates were abstracted into a prior coarse-grained model, which was extended to heterogeneous glycosaminoglycans and small leucine-rich proteoglycans. Exploration of relationships between sequence and shape led to hypotheses that proteoglycan size is dependent on glycosaminoglycan unit composition but independent of sequence permutation. Uronic acid conformational equilibria were modulated by adjacent hexosamine sulfonation and iduronic acid increased glycosaminoglycan chain volume and rigidity, while glucuronic acid imparted chain plasticity. Consequently, block copolymeric glycosaminoglycans contained microarchitectures capable of multivalent binding to growth factors and collagen, with potential for interactional synergy at greater chain number. The described atomic scale views of proteoglycans and heterogeneous glycosaminoglycans provide structural routes to understanding their fundamental signaling and mechanical biological roles and development of new biomaterials.
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Affiliation(s)
- Benedict M Sattelle
- Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology , 131 Princess Street, Manchester, M1 7DN, United Kingdom
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8
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Sattelle BM, Almond A. Microsecond kinetics in model single- and double-stranded amylose polymers. Phys Chem Chem Phys 2014; 16:8119-26. [PMID: 24652085 PMCID: PMC4006424 DOI: 10.1039/c4cp00570h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 03/14/2014] [Indexed: 02/04/2023]
Abstract
Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Starch granule packing, gelation and inclusion-complex formation result from finely balanced macromolecular kinetics that have eluded precise experimental quantification. Here, graphics processing unit (GPU) accelerated multi-microsecond aqueous simulations are employed to explore conformational kinetics in model single- and double-stranded amylose. The all-atom dynamics concur with prior X-ray and NMR data while surprising and previously overlooked microsecond helix-coil, glycosidic linkage and pyranose ring exchange are hypothesized. In a dodecasaccharide, single-helical collapse was correlated with linkages and rings transitioning from their expected syn and (4)C1 chair conformers. The associated microsecond exchange rates were dependent on proximity to the termini and chain length (comparing hexa- and trisaccharides), while kinetic features of dodecasaccharide linkage and ring flexing are proposed to be a good model for polymers. Similar length double-helices were stable on microsecond timescales but the parallel configuration was sturdier than the antiparallel equivalent. In both, tertiary organization restricted local chain dynamics, implying that simulations of single amylose strands cannot be extrapolated to dimers. Unbiased multi-microsecond simulations of amylose are proposed as a valuable route to probing macromolecular kinetics in water, assessing the impact of chemical modifications on helical stability and accelerating the development of new biotechnologies.
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Affiliation(s)
- Benedict M. Sattelle
- Faculty of Life Sciences , Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK . ; Tel: +44 (0)161 306 4199
| | - Andrew Almond
- Faculty of Life Sciences , Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester , M1 7DN , UK . ; Tel: +44 (0)161 306 4199
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9
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Higman VA, Briggs DC, Mahoney DJ, Blundell CD, Sattelle BM, Dyer DP, Green DE, DeAngelis PL, Almond A, Milner CM, Day AJ. A refined model for the TSG-6 link module in complex with hyaluronan: use of defined oligosaccharides to probe structure and function. J Biol Chem 2014; 289:5619-34. [PMID: 24403066 PMCID: PMC3937638 DOI: 10.1074/jbc.m113.542357] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 11/25/2022] Open
Abstract
Tumor necrosis factor-stimulated gene-6 (TSG-6) is an inflammation-associated hyaluronan (HA)-binding protein that contributes to remodeling of HA-rich extracellular matrices during inflammatory processes and ovulation. The HA-binding domain of TSG-6 consists solely of a Link module, making it a prototypical member of the superfamily of proteins that interacts with this high molecular weight polysaccharide composed of repeating disaccharides of D-glucuronic acid and N-acetyl-D-glucosamine (GlcNAc). Previously we modeled a complex of the TSG-6 Link module in association with an HA octasaccharide based on the structure of the domain in its HA-bound conformation. Here we have generated a refined model for a HA/Link module complex using novel restraints identified from NMR spectroscopy of the protein in the presence of 10 distinct HA oligosaccharides (from 4- to 8-mers); the model was then tested using unique sugar reagents, i.e. chondroitin/HA hybrid oligomers and an octasaccharide in which a single sugar ring was (13)C-labeled. The HA chain was found to make more extensive contacts with the TSG-6 surface than thought previously, such that a D-glucuronic acid ring makes stacking and ionic interactions with a histidine and lysine, respectively. Importantly, this causes the HA to bend around two faces of the Link module (resembling the way that HA binds to CD44), potentially providing a mechanism for how TSG-6 can reorganize HA during inflammation. However, the HA-binding site defined here may not play a role in TSG-6-mediated transfer of heavy chains from inter-α-inhibitor onto HA, a process known to be essential for ovulation.
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Affiliation(s)
- Victoria A. Higman
- From the Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - David C. Briggs
- Wellcome Trust Centre for Cell Matrix Research
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - David J. Mahoney
- From the Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Charles D. Blundell
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Benedict M. Sattelle
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Douglas P. Dyer
- Wellcome Trust Centre for Cell Matrix Research
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Dixy E. Green
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
| | - Paul L. DeAngelis
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
| | - Andrew Almond
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Caroline M. Milner
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
| | - Anthony J. Day
- Wellcome Trust Centre for Cell Matrix Research
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT United Kingdom, and
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Sattelle BM, Almond A. Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans. Carbohydr Res 2013; 383:34-42. [PMID: 24252626 PMCID: PMC3909462 DOI: 10.1016/j.carres.2013.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 11/28/2022]
Abstract
Aqueous 10 μs simulations of N-linked mannosyl cores and sialyl Lewis (sLe) antennae are validated. Sequence dependent glycosidic linkage and pyranose ring μs motions are implicated in bioactivity. Stacked pyranoses in sLea and sLex are predicted to be atypically rigid on μs timescales. In a 25 μs simulation of sLex, all known conformers were sampled within the initial 10 μs of dynamics. Unbiased 10 μs simulations are proposed as a route to systematic and accurate glycomic 3D-analysis.
The human glycome comprises a vast untapped repository of 3D-structural information that holds the key to glycan recognition and a new era of rationally designed mimetic chemical probes, drugs, and biomaterials. Toward routine prediction of oligosaccharide conformational populations and exchange rates at thermodynamic equilibrium, we apply hardware-accelerated aqueous molecular dynamics to model μs motions in N-glycans that underpin inflammation and immunity. In 10 μs simulations, conformational equilibria of mannosyl cores, sialyl Lewis (sLe) antennae, and constituent sub-sequences agreed with prior refinements (X-ray and NMR). Glycosidic linkage and pyranose ring flexing were affected by branching, linkage position, and secondary structure, implicating sequence dependent motions in glycomic functional diversity. Linkage and ring conformational transitions that have eluded precise quantification by experiment and conventional (ns) simulations were predicted to occur on μs timescales. All rings populated non-chair shapes and the stacked galactose and fucose pyranoses of sLea and sLex were rigidified, suggesting an exploitable 3D-signature of cell adhesion protein binding. Analyses of sLex dynamics over 25 μs revealed that only 10 μs were sufficient to explore all aqueous conformers. This simulation protocol, which yields conformational ensembles that are independent of initial 3D-structure, is proposed as a route to understanding oligosaccharide recognition and structure–activity relationships, toward development of carbohydrate-based novel chemical entities.
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Affiliation(s)
- Benedict M Sattelle
- Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Andrew Almond
- Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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11
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Blundell CD, Packer MJ, Almond A. Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation. Bioorg Med Chem 2013; 21:4976-87. [PMID: 23886813 PMCID: PMC3744816 DOI: 10.1016/j.bmc.2013.06.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 12/22/2022]
Abstract
Accurate unbound solution 3D-structures of ligands provide unique opportunities for medicinal chemistry and, in particular, a context to understand binding thermodynamics and kinetics. Previous methods of deriving these 3D-structures have had neither the accuracy nor resolution needed for drug design and have not yet realized their potential. Here, we describe and apply a NMR methodology to the aminoglycoside streptomycin that can accurately quantify accessible 3D-space and rank the occupancy of observed conformers to a resolution that enables medicinal chemistry understanding and design. Importantly, it is based upon conventional small molecule NMR techniques and can be performed in physiologically-relevant solvents. The methodology uses multiple datasets, an order of magnitude more experimental data than previous NMR approaches and a dynamic model during refinement, is independent of computational chemistry and avoids the problem of virtual conformations. The refined set of solution 3D-shapes for streptomycin can be grouped into two major families, of which the most populated is almost identical to the 30S ribosomal subunit bioactive shape. We therefore propose that accurate unbound ligand solution conformations may, in some cases, provide a subsidiary route to bioactive shape without crystallography. This experimental technique opens up new opportunities for drug design and more so when complemented with protein co-crystal structures, SAR data and pharmacophore modeling.
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Affiliation(s)
- Charles D Blundell
- C4X Discovery Ltd, Unit 310 Ducie House, Ducie Street, Manchester M1 2JW, UK
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12
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Sattelle BM, Shakeri J, Almond A. Does Microsecond Sugar Ring Flexing Encode 3D-Shape and Bioactivity in the Heparanome? Biomacromolecules 2013; 14:1149-59. [DOI: 10.1021/bm400067g] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Benedict M. Sattelle
- Faculty of Life Sciences, University of Manchester, Manchester
Institute of Biotechnology,
131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Javad Shakeri
- Faculty of Life Sciences, University of Manchester, Manchester
Institute of Biotechnology,
131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Andrew Almond
- Faculty of Life Sciences, University of Manchester, Manchester
Institute of Biotechnology,
131 Princess Street, Manchester, M1 7DN, United Kingdom
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13
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Sattelle BM, Bose-Basu B, Tessier M, Woods RJ, Serianni AS, Almond A. Dependence of pyranose ring puckering on anomeric configuration: methyl idopyranosides. J Phys Chem B 2012; 116:6380-6. [PMID: 22577942 DOI: 10.1021/jp303183y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the aldohexopyranose idose, the unique presence of three axial ring hydroxyl groups causes considerable conformational flexibility, rendering it challenging to study experimentally and an excellent model for rationalizing the relationship between puckering and anomeric configuration. Puckering in methyl α- and β-L-idopyranosides was predicted from kinetically rigorous 10 μs simulations using GLYCAM11 and three explicit water models (TIP3P, TIP4P, and TIP4P-EW). In each case, computed pyranose ring three-bond (vicinal) (1)H-(1)H spin couplings ((3)J(H,H)) trended with NMR measurements. These values, calculated puckering exchange rates and free energies, were independent of the water model. The α- and β-anomers were (1)C(4) chairs for 85 and >99% of their respective trajectories and underwent (1)C(4)→(4)C(1) exchange at rates of 20 μs(-1) and 1 μs(-1). Computed α-anomer (1)C(4)↔(4)C(1) puckering rates depended on the exocyclic C6 substituent, comparing hydroxymethyl with carboxyl from previous work. The slower kinetics and restricted pseudorotational profile of the β-anomer were caused by water occupying a cavity bounded by the anomeric 1-O-methyl and the C6 hydroxymethyl groups. This finding rationalizes the different methyl α- and β-L-idopyranoside (3)J(H,H) values. Identifying a relationship between idopyranose anomeric configuration, microsecond puckering, and water structure facilitates engineering of biologically and commercially important derivatives and underpins deciphering presently elusive structure-function relationships in the glycome.
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Affiliation(s)
- Benedict M Sattelle
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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14
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Isles C, Robertson S, Almond A, Donaldson K, Clark D. The challenges of renal replacement therapy and renal palliative care in the elderly. J R Coll Physicians Edinb 2012; 41:238-43. [PMID: 21949923 DOI: 10.4997/jrcpe.2011.313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The main aim of this review is to let general practitioners and physicians understand what happens to older patients after referral to the renal service. Usually, most patients will be managed completely by the renal team, either because the patient requires dialysis or because conservative but specialised care is appropriate. The recent increase in dialysis rate can mostly be accounted for by older patients for whom such demanding treatment was previously thought to be contraindicated. The decision to dialyse the elderly still remains difficult, with recent data suggesting that if there are significant comorbidities the survival advantage of dialysis in patients over 75 years of age is unlikely to be more than four months. Towards the end of life, conservative treatment is not simply a decision not to dialyse, but comprises active disease management, including treatment of anaemia and other supportive care, which may become increasingly complex, e.g. pain relief with fentanyl and alfentanyl. Older patients who decide to accept dialysis treatment contend with all the usual end of life issues of older people. They have an additional option, denied to the rest of us, of dialysis withdrawal; this effectively allows them to die at a time of their choosing.
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Affiliation(s)
- C Isles
- Department of Medicine, Dumfries & Galloway Royal Infirmary, Dumfries, Scotland.
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15
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16
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Abstract
Understanding microsecond-timescale dynamics is crucial to establish three-dimensional (3D) structure-activity relationships in sugars but has been intractable to experiments and simulations. As a consequence, whether arguably the most important chemical scaffold in glycobiology, N-acetyl-d-glucosamine (GlcNAc), deviates from a rigid (4)C(1) chair is unknown. Here, conformer populations and exchange kinetics were quantified from the longest aqueous carbohydrate simulations to date (0.2 ms total) of GlcNAc, four derivatives from heparan sulfate and their methylglycosides. Unmodified GlcNAc took 3-5 μs to reach a conformational equilibrium, which comprised a metastable (4)C(1) chair that underwent (4)C(1) ↔ (1)C(4) transitions at a predicted forward rate of 0.8 μs(-1) with an average (1)C(4)-chair lifetime of 3 ns. These predictions agree with high-resolution crystallography and nuclear magnetic resonance but not with the hypothesis that GlcNAc is a rigid (4)C(1) chair, concluded from previous experimental analyses and non-aqueous modeling. The methylglycoside was calculated to have a slower forward rate (0.3 μs(-1)) and a more stable (4)C(1) conformer (0.2 kcal mol(-1)), suggesting that pivotal 3D intermediates (particularly (2)S(O), (1)S(5) and B(2,5)) increased in energy, and water was implicated as a major cause. Sulfonation (N-, 3-O and 6-O) significantly augmented this effect by blocking pseudorotation, but did not alter the rotational preferences of hydroyxl or hydroxymethyl groups. We therefore propose that GlcNAc undergoes puckering exchange that is dependent on polymerization and sulfo substituents. Our analyses, and 3D model of the equilibrium GlcNAc conformer in water, can be used as dictionary data and present new opportunities to rationally modify puckering and carbohydrate bioactivity, with diverse applications from improving crop yields to disease amelioration.
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Affiliation(s)
| | - Andrew Almond
- Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
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17
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Abstract
A membrane-spanning bis(meso-3-pyridyl) porphyrin 1 has been synthesized, embedded in EYPC vesicles, and upon Pd(II) addition has been shown to form ionophores that allow the passage of anionic 5/6-carboxyfluorescein through membranes. The geometric matching of bis(meso-3-pyridyl) porphyrin 1 and trans-Pd(II) was designed to give a cyclic porphyrin trimer [PdCl(2)(1)](3). However, solution-phase studies showed that PdCl(2)(PhCN)(2) cross linked 1 into linear oligomers at porphyrin concentrations above 10 mM, although the formation of cyclic species was inferred from studies at concentrations below 2 μM. Fluorescence titrations showed that embedding porphyrin 1 in bilayers greatly reduced its affinity for Pd(II), but the combination of porphyrin 1 and Pd(II) gave an ionophoric species that increased the rate of 5/6-carboxyfluorescein (5/6-CF) transit through the phospholipid bilayer 12-fold. A maximum in the 5/6-CF release rate was observed at a Pd(II) concentration of 4 μM, and the application of a solution-phase binding model to the membrane phase showed that this peak in ionophoric activity corresponded to the greatest extent of porphyrin oligomerization. Further studies suggested these Pd(II)/porphyrin oligomers transported 5/6-CF via a channel mechanism.
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Affiliation(s)
- Usha Devi
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
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18
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Abstract
The pyranose ring of L-iduronic acid (IdoA), a major constituent of the anticoagulant heparin, is an equilibrium of multiple ring puckers that have evaded quantification by experiment or computation. In order to resolve this enigma, we have calculated the free energy landscape of IdoA and two related monosaccharides from extensive microsecond simulations. After establishing that the simulated puckers had reached equilibrium, hypotheses were confirmed that (a) IdoA (1)C(4)- and (4)C(1)-chair conformations exchange on the microsecond time scale, (b) C5 epimerization leads to a (4)C(1)-chair, and (c) IdoA 2-O-sulfation (IdoA2S) stabilizes the (1)C(4) conformer. The IdoA and IdoA2S (1)C(4) conformers were isoenergetic and computed to be 0.9 and 2.6 kcal mol(-1) lower in free energy than their respective (4)C(1)-chair conformations. The simulations also predicted that the IdoA (2)S(O)-skew-boat was less populated than previously thought. Novel chemical synthesis and ultra-high-field NMR supported these observations, but slight discrepancies in observed and predicted NMR vicinal couplings implied that the simulation overestimated the population of the IdoA (4)C(1)-chair with respect to (1)C(4)-chair due to small force field inaccuracies that only manifest in long simulations. These free-energy calculations drive improvements in computational methods and provide a novel route to carbohydrate mimetic biomaterials and pharmaceuticals.
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Affiliation(s)
- Benedict M Sattelle
- Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Yaffe NR, Almond A, Blanch EW. A New Route to Carbohydrate Secondary and Tertiary Structure Using Raman Spectroscopy and Raman Optical Activity. J Am Chem Soc 2010; 132:10654-5. [DOI: 10.1021/ja104077n] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicola R. Yaffe
- Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Andrew Almond
- Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Ewan W. Blanch
- Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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Sattelle DB, Buckingham SD, Akamatsu M, Matsuda K, Pienaar IS, Jones AK, Sattelle BM, Almond A, Blundell CD. Corrigendum to “Comparative pharmacology and computational modelling yield insights into allosteric modulation of human α7 nicotinic acetylcholine receptors” [Biochem. Pharmacol. 78 (2009) 836–843]. Biochem Pharmacol 2010. [DOI: 10.1016/j.bcp.2010.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Teckchandani S, Robertson S, Almond A, Donaldson K, Isles C. Rhabdomyolysis following co-prescription of fusidic acid and atorvastatin. J R Coll Physicians Edinb 2010; 40:33-6. [DOI: 10.4997/jrcpe.2010.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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22
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Sattelle BM, Shakeri J, Roberts IS, Almond A. A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation. Carbohydr Res 2009; 345:291-302. [PMID: 20022001 PMCID: PMC3098369 DOI: 10.1016/j.carres.2009.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 11/06/2009] [Accepted: 11/10/2009] [Indexed: 11/26/2022]
Abstract
The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-structure at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without (15)N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the beta(1-->3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the beta(1-->3) psi dihedral (as previously predicted by simulation), while the beta(1-->4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties.
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Affiliation(s)
- Benedict M Sattelle
- Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN, UK
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23
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Sattelle DB, Buckingham SD, Akamatsu M, Matsuda K, Pienaar IS, Jones AK, Sattelle BM, Almond A, Blundell CD. Comparative pharmacology and computational modelling yield insights into allosteric modulation of human alpha7 nicotinic acetylcholine receptors. Biochem Pharmacol 2009; 78:836-43. [PMID: 19549506 DOI: 10.1016/j.bcp.2009.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/15/2009] [Accepted: 06/15/2009] [Indexed: 11/18/2022]
Abstract
The human alpha7 nicotinic acetylcholine receptor (nAChR) subunit and its Caenorhabditis elegans homolog, ACR-16, can generate functional recombinant homomeric receptors when expressed in Xenopus laevis oocytes. Both nAChRs express robustly in the presence of the co-injected chaperone, RIC-3, and show striking differences in the actions of a type I positive allosteric modulator (PAM), ivermectin (IVM). Type I PAMs are characterised by an increase in amplitude only of the response to acetylcholine (ACh), whereas type II PAMs exhibit, in addition, changes in time-course/desensitization of the ACh response. The type I PAMs, ivermectin, 5-hydroxyindole (5-HI), NS-1738 and genistein and the type II PAM, PNU-120596, are all active on human alpha7 but are without PAM activity on ACR-16, where they attenuate the amplitude of the ACh response. We used the published structure of avermectin B1a to generate a model of IVM, which was then docked into the candidate transmembrane allosteric binding site on alpha7 and ACR-16 in an attempt to gain insights into the observed differences in IVM actions. The new pharmacological findings and computational approaches being developed may inform the design of novel PAM drugs targeting major neurological disorders.
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Affiliation(s)
- David B Sattelle
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK.
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Blundell CD, Roberts IS, Sheehan JK, Almond A. Investigating the molecular basis for the virulence of Escherichia coli K5 by nuclear magnetic resonance analysis of the capsule polysaccharide. J Mol Microbiol Biotechnol 2009; 17:71-82. [PMID: 19401610 DOI: 10.1159/000215933] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The capsular polysaccharide of Escherichia coli K5 has been hypothesised to promote virulence through its molecular mimicry of host heparan sulphate. To test this hypothesis, we have produced pure oligosaccharides from K5 capsular polysaccharide and investigated their conformational properties with ultra-high-field nuclear magnetic resonance (NMR) (900 MHz). Ultra-high-field affords a significant resolution enhancement over previous studies and allowed a full-atomic assignment of the K5 hexasaccharide for the first time. All carbohydrate rings adopt a (4)C(1) conformation, the amide sidechains have a trans orientation and the hydroxymethyl group is freely exposed to bulk solvent. Initial models of the glycosidic linkage conformation based upon simple interpretation of NOE cross-peaks suggests that the beta1-->4 linkage adopts a 3D geometry of phi approximately 60 degrees , psi approximately 0 degrees and the alpha1-->4 linkage prefers phi approximately -30 degrees , psi approximately -30 degrees (phi and psi being defined by dihedral angles involving linkage protons). In this conformation the overall molecular geometries of K5 polysaccharide, heparan sulphate and even fully-sulphated heparin are remarkably similar. These results substantiate the hypothesis that the K5 capsular polysaccharide confers virulence to E. coli K5 by being a 3D molecular mimetic of host heparan sulphate, helping it to evade detection by the mammalian immune system.
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Affiliation(s)
- Charles D Blundell
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
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25
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Mackeen MM, Almond A, Deschamps M, Cumpstey I, Fairbanks AJ, Tsang C, Rudd PM, Butters TD, Dwek RA, Wormald MR. The conformational properties of the Glc3Man unit suggest conformational biasing within the chaperone-assisted glycoprotein folding pathway. J Mol Biol 2009; 387:335-47. [PMID: 19356590 DOI: 10.1016/j.jmb.2009.01.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 01/19/2009] [Accepted: 01/23/2009] [Indexed: 11/16/2022]
Abstract
A major puzzle is: are all glycoproteins routed through the ER calnexin pathway irrespective of whether this is required for their correct folding? Calnexin recognizes the terminal Glcalpha1-3Manalpha linkage, formed by trimming of the Glcalpha1-2Glcalpha1-3Glcalpha1-3Manalpha (Glc3Man) unit in Glc3Man9GlcNAc2. Different conformations of this unit have been reported. We have addressed this problem by studying the conformation of a series of N-glycans; i.e. Glc3ManOMe, Glc3Man(4,5,7)GlcNAc2 and Glc1Man9GlcNAc2 using 2D NMR NOESY, ROESY, T-ROESY and residual dipolar coupling experiments in a range of solvents, along with solution molecular dynamics simulations of Glc3ManOMe. Our results show a single conformation for the Glcalpha1-2Glcalpha and Glcalpha1-3Glcalpha linkages, and a major (65%) and a minor (30%) conformer for the Glcalpha1-3Manalpha linkage. Modeling of the binding of Glc1Man9GlcNAc2 to calnexin suggests that it is the minor conformer that is recognized by calnexin. This may be one of the mechanisms for controlling the rate of recruitment of proteins into the calnexin/calreticulin chaperone system and enabling proteins that do not require such assistance for folding to bypass the system. This is the first time evidence has been presented on glycoprotein folding that suggests the process may be optimized to balance the chaperone-assisted and chaperone-independent pathways.
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Affiliation(s)
- Mukram M Mackeen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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26
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Almond A, Siddiqui S, Robertson S, Norrie J, Isles C. Comparison of combined urea and creatinine clearance and prediction equations as measures of residual renal function when GFR is low. QJM 2008; 101:619-24. [PMID: 18540009 DOI: 10.1093/qjmed/hcn032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND UK, US and European guidelines recommend the decision to initiate dialysis should be based on a combination of measurements of kidney function, nutritional status and clinical symptoms. Such recommendations assume an accurate and reproducible measure of glomerular filtration rate (GFR). METHODS Prospective study of 97 patients with chronic kidney disease (CKD) and serum creatinine >200 micromol/l (2.26 mg/dl) who between them contributed 388 24 h urine collections. Our main outcome measure was the number of patients with low residual renal function identified by different tests, using widely accepted thresholds. We calculated sensitivity, specificity, positive and negative predictive values and receiver operating characteristic curves for each comparison using a combined urea and creatinine clearance of <15 ml/min to indicate the likely presence of end stage renal disease (CKD stage 5). RESULTS Seventy five patients had a combined urea and creatinine clearance <15 ml/min during the study. Using the highest measurement of serum creatinine for each patient, the best of the prediction equations was the 4-variable modification of diet in renal disease (MDRD) equation (area under ROC curve 0.93). This was followed by Kt/V (AUC 0.91) and Cockroft Gault with and without correction for ideal body weight (AUC 0.89). Further analyses showed that the 4-variable MDRD equation had higher NPV (64%) but lower PPV (89%) than the other tests (NPV 40-49%, PPV 92-100%), for identifying patients whose combined clearance was <15 ml/min. CONCLUSION The 4-variable MDRD formula is currently the best available prediction equation for GFR, but will nevertheless over estimate residual renal function when this is significantly impaired in up to 36% cases. Collection of 24 h urine samples may still have a role in the assessment of patients with stages 4 and 5 CKD.
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Affiliation(s)
- A Almond
- Renal Unit, Dumfries and Galloway Royal Infirmary, Dumfries, DG1 4AP, UK.
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27
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Mobli M, Nilsson M, Almond A. The structural plasticity of heparan sulfate NA-domains and hence their role in mediating multivalent interactions is confirmed by high-accuracy (15)N-NMR relaxation studies. Glycoconj J 2007; 25:401-14. [PMID: 18080183 PMCID: PMC2413117 DOI: 10.1007/s10719-007-9081-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Revised: 10/16/2007] [Accepted: 10/18/2007] [Indexed: 10/29/2022]
Abstract
Considering the biological importance of heparan sulfate (HS) and the significant activity of its highly-sulfated regions (S-domains), the paucity of known functions for the non-sulfated NA-domains is somewhat puzzling. It has been suggested that chain dynamics within the NA-domains are the key to their functional role in HS. In this study, we investigate this hypothesis using state-of-the-art nuclear magnetic resonance (NMR) experiments at multiple frequencies. To resolve the problem of severe overlap in (1)H-NMR spectra of repetitive polysaccharides from proteoglycans, we have prepared oligosaccharides with the chemical structure of HS NA-domains containing the (15)N nucleus, which has enough chemical shift dispersion to probe the central residues of octasaccharides at atomic resolution using 600 MHz NMR. By performing NMR relaxation experiments at three magnetic-field strengths, high quality data on internal dynamics and rotational diffusion was obtained. Furthermore, translational diffusion could also be measured by NMR using pulse field gradients. These experimental data were used, in concert with molecular dynamics simulations, to provide information on local molecular shape, greatly aiding our relaxation analyses. Our results, which are more accurate than those presented previously, confirm the higher flexibility of the NA-domains as compared with reported data on S-domains. It is proposed that this flexibility has two functional roles. First, it confers a greater area of interaction from the anchoring point on the core protein for the bioactive S-domains. Secondly, it allows multiple interactions along the same HS chain that are dynamically independent of each other.
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Affiliation(s)
- Mehdi Mobli
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
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Abstract
The polysaccharide hyaluronan is an essential component of the vertebrate extracellular matrix and also produced by viruses, bacteria and fungi. Although the hyaluronan polymer is simply a disaccharide that repeats many thousands of times, it has an amazing array of biological functions and medical uses. For example, it is an efficient space filler that maintains hydration, serves as a substrate for assembly of proteoglycans and cellular locomotion, regulates cellular function and development, and is involved in tumor progression, inflammation and wound healing. Its physical properties and biocompatibility also make it of considerable importance in the development of engineered tissue, biomaterials and in clinical applications.
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Affiliation(s)
- A Almond
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, Princess Street, Manchester, M1 7DN United Kingdom.
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Mobli M, Almond A. N-Acetylated amino sugars: the dependence of NMR 3J(HNH2)-couplings on conformation, dynamics and solvent. Org Biomol Chem 2007; 5:2243-51. [PMID: 17609755 PMCID: PMC2396999 DOI: 10.1039/b705761j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 05/11/2007] [Indexed: 01/12/2023]
Abstract
N-Acetylated amino sugars are essential components of living organisms, but their dynamic conformational properties are poorly understood due to a lack of suitable experimental methodologies. Nuclear magnetic resonance (NMR) is ideally suited to these conformational studies, but accurate equations relating the conformation of key substituents (e.g., the acetamido group) to NMR observables are unavailable. To address this, density functional theory (DFT) methods have been used to calculate vicinal coupling constants in N-acetylated amino sugars and derive empirical Karplus equations for (3)J(H(N)H(2)) of N-acetyl-D-glucosamine (GlcNAc) and N-acetyl-D-galactosamine (GalNAc). The fitted Karplus parameters were found to be similar to those previously derived for peptide amide groups, but are consistently larger in magnitude. Local intramolecular interactions had a small effect on the calculated J-couplings and comparison with experimental data suggested that DFT slightly overestimated them. An implicit solvation model consistently lowered the magnitude of the calculated values, improving the agreement with the experimental data. However, an explicit solvent model, while having a small effect, worsened the agreement with experimental data. The largest contributor to experimentally-determined (3)J(H(N)H(2))-couplings is proposed to be librations of the amide group, which are well approximated by a Gaussian distribution about a mean dihedral angle. Exemplifying the usefulness of our derived Karplus equations, the libration of the amide group could be estimated in amino sugars from experimental data. The dynamical spread of the acetamido group in free alpha-GlcNAc, beta-GlcNAc and alpha-GalNAc was estimated to be 32 degrees , 42 degrees and 20 degrees , with corresponding mean dihedral angles of 160 degrees , 180 degrees and 146 degrees , respectively.
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Affiliation(s)
- Mehdi Mobli
- Manchester Interdisciplinary Biocentre, 131 Princess Street, University of Manchester, Manchester, UK M1 7DN. ; Fax: +44 161 30 68918; Tel: +44 161 30 64199
| | - Andrew Almond
- Manchester Interdisciplinary Biocentre, 131 Princess Street, University of Manchester, Manchester, UK M1 7DN. ; Fax: +44 161 30 68918; Tel: +44 161 30 64199
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30
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Abstract
Temperature coefficients (Deltadelta/DeltaT) of amide chemical shifts of N-acetylglucosamine residues have been measured in a range of oligosaccharides of the important vertebrate polysaccharide hyaluronan. Odd- and even-numbered oligosaccharides with glucuronic acid, Delta-4,5-unsaturated glucuronic acid and N-acetylglucosamine at the termini were investigated. All amide proton temperature coefficients were only slightly less negative (-6.9 to - 9.1 ppb/ degrees C) than those of amide protons in free exchange with water (approximately equal to -11 ppb/ degrees C), indicating an absence of persistent intramolecular hydrogen bonds. With the exception of amide groups in reducing-terminal N-acetylglucosamine rings, all amide proton environments have the same temperature coefficient (-6.9 ppb/ degrees C), irrespective of differences in amide group chemical shifts and (3)J(HH) coupling constants, i.e. they do not sense subtle differences in orientation of the amide group. Amide nitrogen temperature coefficients report the same phenomena but with greater sensitivity. These data provide a set of reference values for temperature coefficients measured in other carbohydrates with acetamido sugars.
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Affiliation(s)
- Charles D Blundell
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Princess Street, Manchester M1 7DN, UK
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31
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Blundell CD, Mahoney DJ, Cordell MR, Almond A, Kahmann JD, Perczel A, Taylor JD, Campbell ID, Day AJ. Determining the molecular basis for the pH-dependent interaction between the link module of human TSG-6 and hyaluronan. J Biol Chem 2007; 282:12976-88. [PMID: 17307731 DOI: 10.1074/jbc.m611713200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TSG-6 is an inflammation-associated hyaluronan (HA)-binding protein that has anti-inflammatory and protective functions in arthritis and asthma as well as a critical role in mammalian ovulation. The interaction between TSG-6 and HA is pH-dependent, with a marked reduction in affinity on increasing the pH from 6.0 to 8.0. Here we have investigated the mechanism underlying this pH dependence using a combined approach of site-directed mutagenesis, NMR, isothermal titration calorimetry and microtiter plate assays. Analysis of single-site mutants of the TSG-6 Link module indicated that the loss in affinity above pH 6.0 is mediated by the change in ionization state of a histidine residue (His(4)) that is not within the HA-binding site. To understand this in molecular terms, the pH-dependent folding profile and the pK(a) values of charged residues within the Link module were determined using NMR. These data indicated that His(4) makes a salt bridge to one side-chain oxygen atom of a buried aspartate residue (Asp(89)), whereas the other oxygen is simultaneously hydrogen-bonded to a key HA-binding residue (Tyr(12)). This molecular network transmits the change in ionization state of His(4) to the HA-binding site, which explains the loss of affinity at high pH. In contrast, simulations of the pH affinity curves indicate that another histidine residue, His(45), is largely responsible for the gain in affinity for HA between pH 3.5 and 6.0. The pH-dependent interaction of TSG-6 with HA (and other ligands) provides a means of differentially regulating the functional activity of this protein in different tissue microenvironments.
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Affiliation(s)
- Charles D Blundell
- Medical Research Council Immunochemistry Unit, University of Oxford, South Parks Road, Oxford, UK
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Seyfried NT, Atwood JA, Yongye A, Almond A, Day AJ, Orlando R, Woods RJ. Fourier transform mass spectrometry to monitor hyaluronan-protein interactions: use of hydrogen/deuterium amide exchange. Rapid Commun Mass Spectrom 2007; 21:121-31. [PMID: 17154353 PMCID: PMC4189122 DOI: 10.1002/rcm.2817] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The use of Fourier transform mass spectrometry (FTMS) to monitor noncovalent complex formation in the gas phase under native conditions between the Link module from human tumor necrosis factor stimulated gene-6 (Link_TSG6) and hyaluronan (HA) oligosaccharides is reported. In particular, a titration experiment with increasing concentrations of octasaccharide (HA(8)) to protein produced a noncovalent complex with 1:1 stoichiometry when the oligosaccharide was in molar excess. However, in the presence of a molar excess of tetrasaccharide (HA(4)) nearly all proteins and oligosaccharides were observed in their unbound charge states. These results are consistent with solution-phase properties for this interaction in which HA(8), but not HA(4), supports high affinity Link_TSG6 binding. Hydrogen/deuterium amide exchange mass spectrometry (H/D-EX MS) was also utilized to investigate the level of global deuterium incorporation, over time, for Link_TSG6 in both the absence and presence of HA(8). After dilution into quenching conditions, deuterium incorporation reached limiting asymptotic values of 37 and 26 deuterons for the free and bound protein at 240 and 480 min, respectively, indicating that the oligosaccharide interferes with amide exchange on binding. To detect sequence-specific deuterium incorporation, pepsin digestion of Link_TSG6 in both the absence and presence of HA(8) was performed. A level of deuterium incorporation of 10-30% was observed for peptides analyzed in free Link_TSG6. Interestingly, HA(8) blocked some sites of proteolysis in Link_TSG6 compared to the free protein. Molecular modeling indicated that amino acids proximal to the ligand correlated with regions of the protein that were resistant to enzymatic digestion. Of the peptides that could be analyzed by H/D-EX MS in the presence of the ligand, a 30-60% reduction in deuterium incorporation, relative to the free protein, was observed, even for those sequences not directly involved in HA binding. These results support the utility of FTMS as a method for the characterization of protein-carbohydrate interactions.
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Affiliation(s)
- Nicholas T. Seyfried
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - James A. Atwood
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Austin Yongye
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Andrew Almond
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Anthony J. Day
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Ron Orlando
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
- Correspondence to: R. J. Woods, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
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Almond A, Blundell CD, Higman VA, MacKerell, AD, Day AJ. Using Molecular Dynamics Simulations To Provide New Insights into Protein Structure on the Nanosecond Timescale: Comparison with Experimental Data and Biological Inferences for the Hyaluronan-Binding Link Module of TSG-6. J Chem Theory Comput 2006; 3:1-16. [DOI: 10.1021/ct600236q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Almond
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Princess Street, Manchester M1 7DN, U.K., Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K., MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K., and Department of Pharmaceutical Chemistry, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201
| | - Charles D. Blundell
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Princess Street, Manchester M1 7DN, U.K., Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K., MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K., and Department of Pharmaceutical Chemistry, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201
| | - Victoria A. Higman
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Princess Street, Manchester M1 7DN, U.K., Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K., MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K., and Department of Pharmaceutical Chemistry, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201
| | - Alexander D. MacKerell,
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Princess Street, Manchester M1 7DN, U.K., Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K., MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K., and Department of Pharmaceutical Chemistry, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201
| | - Anthony J. Day
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Princess Street, Manchester M1 7DN, U.K., Michael Smith Building, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K., MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K., and Department of Pharmaceutical Chemistry, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201
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Blundell CD, Reed MAC, Almond A. Complete assignment of hyaluronan oligosaccharides up to hexasaccharides. Carbohydr Res 2006; 341:2803-15. [PMID: 17056022 DOI: 10.1016/j.carres.2006.09.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 09/18/2006] [Accepted: 09/27/2006] [Indexed: 11/16/2022]
Abstract
The glycosaminoglycan hyaluronan is involved in a diverse range of physiological and diseases processes and comprises repeated disaccharide units of N-acetyl-d-glucosamine (GlcNAc) and d-glucuronic acid (GlcA). A molecular description of the solution conformation of HA is required to account for this biology, which is best attained using nuclear magnetic resonance (NMR). NMR studies of the polymer, however, are frustrated by resonance overlap arising from the highly degenerate structure. In contrast, end-effects in oligosaccharides can produce some chemical shift dispersion, giving the possibility that their conformational properties can be measured and extrapolated to models of the polymer. We report the complete resolution and assignment of (1)H, (13)C and (15)N nuclei in hyaluronan oligosaccharides with seven different naturally occurring terminal rings. At 900MHz, all (1)H nuclei in the hexasaccharide GlcA-beta-(1-->3)-GlcNAc-beta-(1-->4)-GlcA-beta-(1-->3)-GlcNAc-beta-(1-->4)-GlcA-beta-(1-->3)-GlcNAc-OH were uniquely resolved and the two central rings were found to be a good model for the polymer environment. These assignments now allow resolved, unambiguous structural restraints to be acquired on this oligosaccharide and extrapolated to models for the solution conformation of the polymer.
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Affiliation(s)
- Charles D Blundell
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Princess Street, Manchester M1 7DN, UK
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Jing W, Haller FM, Almond A, DeAngelis PL. Defined megadalton hyaluronan polymer standards. Anal Biochem 2006; 355:183-8. [PMID: 16842731 DOI: 10.1016/j.ab.2006.06.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2006] [Revised: 06/02/2006] [Accepted: 06/05/2006] [Indexed: 11/23/2022]
Abstract
The utility of polymer standards for the calibration of average molecular mass estimates often is limited by the polydispersity--the breadth of the size distribution--of the standard. Here monodisperse synthetic hyaluronan (or hyaluronic acid [HA]) complexes in the approximately 1- to 8-megadalton (MDa) range were prepared in two steps. First, synchronized stoichiometrically controlled in vitro reactions yielded linear narrow size distribution biotinylated HA chains. Second, streptavidin protein was added at substoichiometric levels to prepare a series of complexes with one, two, three, or four HA chains per streptavidin molecule. The dendritic-like molecules approximate the mobility of natural linear HA chains on agarose gels, making the complexes useful as defined size standards for high-molecular weight HA preparations.
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Affiliation(s)
- Wei Jing
- Hyalose LLC, Oklahoma City, OK 73104, USA
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Blundell CD, Reed MA, Overduin M, Almond A. NMR spectra of oligosaccharides at ultra-high field (900 MHz) have better resolution than expected due to favourable molecular tumbling. Carbohydr Res 2006; 341:1985-91. [PMID: 16784734 PMCID: PMC1828614 DOI: 10.1016/j.carres.2006.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 05/17/2006] [Accepted: 05/21/2006] [Indexed: 11/25/2022]
Abstract
Nuclear magnetic resonance (NMR) remains the most promising technique for acquiring atomic-resolution information in complex carbohydrates. Significant obstacles to the acquisition of such data are the poor chemical-shift dispersion and artifacts resultant from their degenerate chemical structures. The recent development of ultra-high-field NMR (at 900 MHz and beyond) gives new potential to overcome these problems, as we demonstrate on a hexasaccharide of the highly repetitive glycosaminoglycan hyaluronan. At 900 MHz, the expected increase in spectral dispersion due to higher resonance frequencies and reduction in strong coupling-associated distortions are observed. In addition, the fortuitous molecular tumbling rate of oligosaccharides results in longer T2-values that further significantly enhances resolution, an effect not available to proteins. Combined, the resolution enhancement can be as much as twofold relative to 600 MHz, allowing all 1H-resonances in the hexasaccharide to be unambiguously assigned using standard natural-abundance experiments. The use of ultra-high-field spectrometers is clearly advantageous and promises a new and exciting era in carbohydrate structural biology.
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Affiliation(s)
- Charles D. Blundell
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, Princess Street, Manchester M1 7ND, UK
| | - Michelle A.C. Reed
- The Henry Wellcome Building for Biomolecular NMR Spectroscopy, CR-UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
| | - Michael Overduin
- The Henry Wellcome Building for Biomolecular NMR Spectroscopy, CR-UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew Almond
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, Princess Street, Manchester M1 7ND, UK
- Corresponding author. Tel.: +44 161 30 64 199; fax: +44 161 236 0409.
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Blundell C, Deangelis P, Almond A. Hyaluronan: the absence of amide-carboxylate hydrogen bonds and the chain conformation in aqueous solution are incompatible with stable secondary and tertiary structure models. Biochem J 2006; 396:487-98. [PMID: 16506956 PMCID: PMC1482818 DOI: 10.1042/bj20060085] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 02/22/2006] [Accepted: 03/01/2006] [Indexed: 11/17/2022]
Abstract
Contradictory descriptions for the aqueous solution conformation of the glycosaminoglycan hyaluronan (HA) exist in the literature. According to hydrodynamic and simulation data, HA molecules are stiffened by a rapidly interchanging network of transient hydrogen bonds at the local level and do not significantly associate at the global level. In marked contrast, models derived from NMR data suggest that the secondary structure involves persistent hydrogen bonds and that strong associations between chains can occur to form vast stable tertiary structures. These models require an extended 2-fold helical conformation of the HA chain and specific hydrogen bonds between amide and carboxylate groups. To test these descriptions, we have used 15N-labelled oligosaccharides and high-field NMR to measure pertinent properties of the acetamido group. The amide proton chemical shift perturbation and carboxylate group pK(a) value are inconsistent with a highly populated hydrogen bond between the amide and carboxylate groups. Amide proton temperature coefficients and chemical exchange rates confirm this conclusion. Comparison of oligomer properties with polymeric HA indicates that there is no discernible difference in amide proton environment between the centre of octasaccharides and the polymer, inconsistent with the formation of tertiary structures. A [1H-1H-15N] NOESY-HSQC (heteronuclear single-quantum correlation) spectrum recorded on an HA octasaccharide revealed that amide groups in the centre are in a trans orientation and that the average solution conformation is not an extended 2-fold helix. Therefore the two key aspects of the secondary and tertiary structure models are unlikely to be correct. Rather, these new NMR data agree with descriptions from hydrodynamic and simulations data.
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Key Words
- carboxylate pka
- hyaluronan
- hydrogen bond
- 15n-labelled carbohydrate
- structure model
- temperature coefficient
- dyn, dynamic model for secondary structure
- glca, d-glucuronic acid
- glcnac, n-acetyl-d-glucosamine
- ha, hyaluronan
- hsqc, heteronuclear single-quantum correlation
- noe, nuclear overhauser effect
- p.p.b., parts per billion
- tf-inter-s, tertiary structure model involving an extended 2-fold helical conformation, intermolecular hydrogen bonds and hydrophobic stacking interactions
- tf-intra, secondary structure model involving an extended 2-fold helical conformation and intramolecular hydrogen bonds
- tf-wb, secondary structure model involving an extended 2-fold helical conformation and stably bound bridging water molecules
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Affiliation(s)
- Charles D. Blundell
- *Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7ND, U.K
| | - Paul L. Deangelis
- †Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, OK 73104, U.S.A
| | - Andrew Almond
- *Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7ND, U.K
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Blundell CD, Almond A. Enzymatic and chemical methods for the generation of pure hyaluronan oligosaccharides with both odd and even numbers of monosaccharide units. Anal Biochem 2006; 353:236-47. [PMID: 16624243 DOI: 10.1016/j.ab.2006.03.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 03/06/2006] [Accepted: 03/07/2006] [Indexed: 10/24/2022]
Abstract
Hyaluronan oligosaccharides display physiological activities not associated with the polymer and are widely used to characterize hyaluronan-binding proteins. They can also be used as biocompatible starting blocks for chemical derivatization. Here we present methods for generating milligram quantities of unusual odd- and even-numbered oligosaccharides, greatly increasing the diversity of reagents for use in such studies. These methods are based upon protocols from the 1960s, at which time it was very difficult to assess the stereochemical purity of the products. To address this, products were analyzed with modern high-field nuclear magnetic resonance spectroscopy. Alkaline beta-elimination conditions previously used to remove reducing-terminal N-acetylglucosamine residues in fact introduce a significant ( approximately 30%) level of stereoisomerism in the products by alkali-catalyzed keto-enol tautomerizations. Milder alkaline conditions were used to overcome this problem, reducing the contamination to <5%. The elimination by-products from this reaction were isolated and characterized, allowing the mechanism of alkaline degradation of hyaluronan to be investigated for the first time. beta-Glucuronidase was used to remove nonreducing-terminal glucuronic acid residues from oligosaccharides. Odd-numbered oligosaccharides with terminal glucuronic acid residues isolated from hyaluronidase digests are shown to originate from acid-catalyzed acetal hydrolysis during boiling denaturation and also have significant levels of stereochemical impurities.
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Affiliation(s)
- Charles D Blundell
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, Princess Street, Manchester, M1 7ND, UK
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Almond A, Deangelis PL, Blundell CD. Hyaluronan: The Local Solution Conformation Determined by NMR and Computer Modeling is Close to a Contracted Left-handed 4-Fold Helix. J Mol Biol 2006; 358:1256-69. [PMID: 16584748 DOI: 10.1016/j.jmb.2006.02.077] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 01/27/2006] [Accepted: 02/28/2006] [Indexed: 11/27/2022]
Abstract
The polysaccharide hyaluronan (HA) is a ubiquitous component of the vertebrate extracellular matrix with diverse physiological roles from space-filling to acting as a scaffold for other macromolecules. The molecular interactions responsible for these solution properties have been the subject of much debate and, primarily due to the lack of residue-specific experimental data, no consensus model for the three-dimensional conformation nor dynamics of HA in solution has emerged. Here, the solution conformation of HA is investigated using molecular dynamics (MD) simulations and high-field nuclear magnetic resonance (NMR). In contrast to previous studies, MD simulations incorporated explicit water molecules and sodium ions, while NMR experiments utilized (15)N-enriched oligosaccharides to allow residue-specific information to be obtained. The resultant average conformation is predicted to be almost a contracted left-handed 4-fold helix; i.e. similar to that observed for sodium hyaluronate fibers by X-ray diffraction, but with the acetamido side-chain trans to H(2). The glycosidic linkages and acetamido side-chains are predicted to have standard deviation rotations of 13 degrees and 18 degrees around their mean conformations in free solution, respectively, and are not observed to be stabilized by strong intramolecular hydrogen bonds as X-ray fiber diffraction refinements describe for the solid-state. Rather, weak and transient hydrogen bonds that are in rapid interchange with solvent molecules are predicted. These predictions are quantitatively consistent with demanding residue-specific NMR data and correspond to an HA molecule that is rod-like as an oligosaccharide and behaves as a stiffened random coil at large molecular mass, in close agreement with previous hydrodynamic observations. This new description of the solution conformation of HA is consistent with all available experimental data and accounts for its viscoelastic space-filling properties. This representation can be used as a basis for modeling the association between HA and proteins, which will elucidate important aspects of extracellular matrix assembly.
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Affiliation(s)
- Andrew Almond
- Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, Princess Street, Manchester, M1 7ND, UK.
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Seyfried NT, Day AJ, Almond A. Experimental evidence for all-or-none cooperative interactions between the G1-domain of versican and multivalent hyaluronan oligosaccharides. Matrix Biol 2006; 25:14-9. [PMID: 16185858 DOI: 10.1016/j.matbio.2005.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 08/22/2005] [Accepted: 08/22/2005] [Indexed: 11/27/2022]
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Mackeen M, Almond A, Cumpstey I, Enis SC, Kupce E, Butters TD, Fairbanks AJ, Dwek RA, Wormald MR. The importance of including local correlation times in the calculation of inter-proton distances from NMR measurements: ignoring local correlation times leads to significant errors in the conformational analysis of the Glcα1–2Glcα linkage by NMR spectroscopy. Org Biomol Chem 2006; 4:2241-6. [PMID: 16729133 DOI: 10.1039/b604126d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The experimental determination of oligosaccharide conformations has traditionally used cross-linkage 1H-1H NOE/ROEs. As relatively few NOEs are observed, to provide sufficient conformational constraints this method relies on: accurate quantification of NOE intensities (positive constraints); analysis of absent NOEs (negative constraints); and hence calculation of inter-proton distances using the two-spin approximation. We have compared the results obtained by using 1H 2D NOESY, ROESY and T-ROESY experiments at 500 and 700 MHz to determine the conformation of the terminal Glc alpha1-2Glc alpha linkage in a dodecasaccharide and a related tetrasaccharide. For the tetrasaccharide, the NOESY and ROESY spectra produced the same qualitative pattern of linkage cross-peaks but the quantitative pattern, the relative peak intensities, was different. For the dodecasaccharide, the NOESY and ROESY spectra at 500 MHz produced a different qualitative pattern of linkage cross-peaks, with fewer peaks in the NOESY spectrum. At 700 MHz, the NOESY and ROESY spectra of the dodecasaccharide produced the same qualitative pattern of peaks, but again the relative peak intensities were different. These differences are due to very significant differences in the local correlation times for different proton pairs across this glycosidic linkage. The local correlation time for each proton pair was measured using the ratio of the NOESY and T-ROESY cross-relaxation rates, leaving the NOESY and ROESY as independent data sets for calculating the inter-proton distances. The inter-proton distances calculated including the effects of differences in local correlation times give much more consistent results.
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Affiliation(s)
- Mukram Mackeen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Colebrooke SA, Blundell CD, DeAngelis PL, Campbell ID, Almond A. Exploiting the carboxylate chemical shift to resolve degenerate resonances in spectra of 13C-labelled glycosaminoglycans. Magn Reson Chem 2005; 43:805-15. [PMID: 15996005 DOI: 10.1002/mrc.1620] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glycosaminoglycans (GAG) are important vertebrate extracellular matrix polysaccharides that comprise repeated units of an acidic and an N-acetylated sugar. The constituent acidic sugars are central to their biological functions, but have been largely inaccessible to NMR because the (1)H resonances overlap with those from other residues. Here, pulse sequences that address this failure are developed using (13)C-enriched oligosaccharides of the glycosaminoglycan, hyaluronan, as model systems. Two pulse sequences are presented that exploit the unique chemical shifts and scalar couplings present at the carboxylate moiety to filter out coherences from the N-acetylated sugars and produce simple spectra containing only resonances from the acidic sugars. The first sequence uses one-bond couplings to correlate the carboxylate carbon with the adjacent carbon and its directly attached proton, while the second sequence exploits a long-range coupling to correlate the carboxylate carbon with the anomeric proton and carbon of the same residue. In addition, inclusion of an isotropic mixing block into these sequences allows resonances from the otherwise degenerate ring protons to be resolved. Spectra from the hyaluronan tetra- and hexasaccharides show that all glucuronic acid (GlcA) residues can be resolved from one another, allowing nuclei to be assigned in a sequence-specific manner. However, in some spectra, resonances are observed at positions not predicted by spin-operator analysis, and simulations reveal that these additional magnetisation transfers result from strong-coupling. These experiments represent a foundation from which new structural and biochemical information can be obtained in a sequence-specific manner for the acidic sugar residues in hyaluronan and other glycosaminoglycans.
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Affiliation(s)
- Simon A Colebrooke
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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Blundell CD, Almond A, Mahoney DJ, DeAngelis PL, Campbell ID, Day AJ. Towards a Structure for a TSG-6·Hyaluronan Complex by Modeling and NMR Spectroscopy. J Biol Chem 2005; 280:18189-201. [PMID: 15718240 DOI: 10.1074/jbc.m414343200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Link module from human TSG-6, a hyaladherin with roles in ovulation and inflammation, has a hyaluronan (HA)-binding groove containing two adjacent tyrosine residues that are likely to form CH-pi stacking interactions with sequential rings in the sugar. We have used this observation to construct a model of a protein.HA complex, which was then tested against existing experimental information and by acquisition of new NMR data sets of [(13)C, (15)N]HA (8-mer) complexed with unlabeled protein. A major finding of this analysis was that acetamido side chains of two GlcNAc rings fit into hydrophobic pockets on either side of the adjacent tyrosines, providing a selectivity mechanism of HA over other polysaccharides. Furthermore, two basic residues have a separation that matches that of glucuronic acids in the sugar, consistent with the formation of salt bridges; NMR experiments at a range of pH values identified protein groups that titrate due to their proximity to a free carboxylate in HA. Sequence alignment and construction of homology models for all human Link modules in their HA-bound states revealed that many of these features are conserved across the superfamily, thus allowing the prediction of functionally important residues. In the case of cartilage link protein, its two Link modules were docked together (using bound HA as a guide), identifying hydrophobic residues likely to form an intra-Link module interface as well as amino acids that could be involved in supporting intermolecular interactions between link proteins and chondroitin sulfate proteoglycans. Here, we propose a mechanism for ternary complex formation that generates higher order helical structures, as may exist in cartilage aggregates.
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Affiliation(s)
- Charles D Blundell
- Medical Research Council Immunochemistry Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
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Abstract
Complex carbohydrates are implicated in many important biological processes, and have a strong interaction with water. This close interplay with molecular water through multiple hydroxyls may be an integral part of their emergent structure and dynamics, as selected during evolution. Using molecular dynamics simulations with explicit water the interactions at the linkages within a variety of oligosaccharides are investigated and contrasted, in order to establish correlations between linkage orientation, sugar epimerization, and water interaction. In particular, interactions at alpha linkages, and between mannose and glucose residues, that are common in oligosaccharides are considered. Sugars joined by alpha linkages at the 2-, 3-, and 6-position were found to interact via a combination of weak hydrogen-bonds and water-bridges, which is dependent on the epimerization state of the sugars. Due to their three-dimensional structure, they are also likely to interact with noncontiguous sugar residues in an oligosaccharide, which can lead to ordered structures through the exclusion of water. On the other hand, beta linkages (to 3- and 4-position) maintain strong hydrogen-bonds, have a limited ability to be involved in water-bridges, and predominantly interact with the directly attached sugars. Therefore, sequences of alpha-linked sugars form compact, branched structures that have conformational flexibility, and beta linkages form extended, relatively rigid structures, suitable for structural molecules, and at the termini of protein bound oligosaccharides. These results provide further tentative ties between chemical structure, water interactions, and the emergent form and function of specific sugars and linkages in oligosaccharides.
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Affiliation(s)
- Andrew Almond
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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45
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Abstract
Complex carbohydrates are considered to be flexible biomolecules, yet few experimental techniques are available to characterize their dynamics. In this study, we investigate the potential of 15N relaxation to probe the dynamics of hyaluronan oligosaccharides by adapting approaches previously applied to proteins. Unlike the 13C nucleus, 15N provides considerably enhanced spectral resolution, allowing position-specific information to be measured even in the middle of oligomers as large as decasaccharides. Moreover, isotopic incorporation maintains the 1H-15N group as an isolated spin-pair, allowing relaxation experiments to be performed and interpreted at low concentrations. A methodology is described for calculating the Lipari and Szabo model-free parameters at specific positions in hyaluronan oligomers and is used to produce a dynamic representation for the hexasaccharide. In this model, the glycosidic linkages and acetamido rotamer were determined to deviate by 18 degrees and 24 degrees from their mean positions, respectively. This approach allows the dynamic structural characterization of hyaluronan and other nitrogen-containing carbohydrates. The resultant models provide crucial insights into the physical properties and biology of these flexible molecules, which are at present poorly understood.
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Affiliation(s)
- Andrew Almond
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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46
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Seyfried NT, McVey GF, Almond A, Mahoney DJ, Dudhia J, Day AJ. Expression and purification of functionally active hyaluronan-binding domains from human cartilage link protein, aggrecan and versican: formation of ternary complexes with defined hyaluronan oligosaccharides. J Biol Chem 2004; 280:5435-48. [PMID: 15590670 DOI: 10.1074/jbc.m411297200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The chondroitin sulfate proteoglycan aggrecan forms link protein-stabilized complexes with hyaluronan (HA), via its N-terminal G1-domain, that provide cartilage with its load bearing properties. Similar aggregates (potentially containing new members of the link protein family), in which other chondroitin sulfate proteoglycans (i.e. versican, brevican, and neurocan) substitute for aggrecan, may contribute to the structural integrity of many other tissues including skin and brain. In this study, cartilage link protein (cLP) and the G1-domains of aggrecan (AG1) and versican (VG1) were expressed in Drosophila S2 cells. The recombinant human proteins were found to have properties similar to those described for the native molecules (e.g. cLP was able to form oligomers, and HA decasaccharides were the minimum size that could compete effectively for their binding to polymeric HA). Gel filtration and protein cross-linking/matrix-assisted laser desorption ionization time-of-flight peptide fingerprinting showed that cLP and AG1 interact in the absence or presence of HA. Conversely, cLP and VG1 did not bind directly to each other in solution yet formed ternary complexes with HA24. N-linked glycosylation of AG1 and VG1 was demonstrated to be unnecessary for either HA binding or the formation of ternary complexes. Surprisingly, the length of HA required to accommodate two G1-domains was found to be significantly larger for aggrecan than versican, which may reflect differences in the conformation of HA stabilized on binding these proteins.
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Affiliation(s)
- Nicholas T Seyfried
- Medical Research Council Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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47
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Abstract
We report the production of biologically active hyaluronan (HA) oligosaccharides labeled with the fluorophore 2-aminobenzoic acid (2AA). Oligosaccharides from 4 to 40 residues in length were purified to homogeneity by ion exchange chromatography using a logarithmic gradient. Molecular weight and purity characterization of HA oligosaccharides is facilitated by 2AA derivatization because it enhances signals in MALDI-TOF MS and improves FACE (fluorophore-assisted carbohydrate electrophoresis) analysis by avoiding the inverted parabolic migration characteristic of 2-aminoacridone (AMAC)-labeled sugars. The small size and shape of the fluorophore maintains the biological activity of the derivatized oligosaccharides, as demonstrated by their ability to compete for polymeric HA binding to the G1-domain of human recombinant versican (VG1). An electrophoretic mobility shift assay was used to study VG1 binding to labeled HA 8-, 10-, 20-, 30-, and 40-mers, and although no stable VG1 binding was observed to labeled 8-mers, the equilibrium dissociation constant (100 nM) for VG1 with HA(10) was estimated from densitometry analysis of the free oligosaccharide. Interactions involving HA 20-, 30-, and 40-mers (proposed to be multivalent) could also be studied using this protocol. Oligosaccharides labeled with 2AA therefore show excellent potential as probes in fluorescence-based assays that investigate protein-carbohydrate interactions.
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Affiliation(s)
- Nicholas T Seyfried
- MRC Immunochemistry Unit, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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48
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Blundell CD, DeAngelis PL, Day AJ, Almond A. Use of 15N-NMR to resolve molecular details in isotopically-enriched carbohydrates: sequence-specific observations in hyaluronan oligomers up to decasaccharides. Glycobiology 2004; 14:999-1009. [PMID: 15215231 DOI: 10.1093/glycob/cwh117] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The glycosaminoglycan hyaluronan is a vital structural component of extracellular matrices with diverse biological functions, a molecular understanding of which requires a detailed description of secondary and tertiary solution structures. Various models of these structures have been proposed on the basis of 1H and 13C natural-abundance nuclear magnetic resonance (NMR) experiments, but resonance overlap limits further progress with these techniques. We have therefore produced 15N- and 13C- isotopically-labeled hyaluronan oligosaccharides and applied triple-resonance and 3D experiments to overcome this restriction. Spectra recorded on oligosaccharides (of lengths 4, 6, 8, 10, and 12 sugar rings), reveal that the 15N nucleus allows resolution of the amide groups in a decamer at high magnetic field, whereas 13C natural-abundance NMR can only resolve internal groups up to hexamers. Complete 13N sequence- specific assignments of these oligosaccharides indicate that the chemical shift dispersion can be explained by end-effects, which are seen even in the middle of octamers. Triple- resonance and 15N-edited 3D experiments, among the first of their kind in oligosaccharides, have been used to achieve resolution of ring 1H and 13C nuclei where not possible previously. The subtle chemical shift perturbations resolved suggest that different conformations and dynamics occur at the ends, which may contribute to the range of biological activities displayed by varying lengths of hyaluronan. 15N-NMR in carbohydrates has not received much attention before, however, this study demonstrates it has clear advantages for achieving resolution and assessing dynamic motion. These conclusions are likely to be applicable to the study of the structure and dynamics of other nitrogen-containing carbohydrates.
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Affiliation(s)
- Charles D Blundell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1, 3QU, UK
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49
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Abstract
Fucosylated O- and N-linked glycans are essential recognition molecules in plants and animals. To understand how they impart their functions, through interactions with proteins, requires a detailed analysis of structure and dynamics, but this is presently lacking. In this study, the three-dimensional structure and dynamics of three fucosylated oligosaccharides are investigated using a combination of high field (800 MHz) nuclear magnetic resonance and long (50 ns) molecular dynamics simulations in explicit water. Predictions from dynamics simulations were in agreement with nuclear Overhauser cross-peak intensities. Similarly, a theory of weak alignment in neutral media resulted in reasonable predictions of residual dipolar couplings for the trisaccharide fucosyllactose. However, for larger penta- and hexasaccharides (LNF-1 and LND-1), the anisotropic component of the alignment was underestimated, attributed to shape irregularities of the fucosyl branches on an otherwise linear core, being more pronounced in a singly branched than a doubly branched oligosaccharide. Simulations, confirmed by experiment, predicted fucosylated molecules that are restricted to librations about a single average conformation. This restriction is partly due to microscopic water interactions, which act to stabilize intramolecular hydrogen bonds and maintain tight and ordered conformations; a view not forthcoming from simpler, nonaqueous simulations. Such a conclusion is crucial for understanding how these molecules interact with proteins and impart their recognition properties.
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Affiliation(s)
- Andrew Almond
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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50
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Blundell CD, Mahoney DJ, Almond A, DeAngelis PL, Kahmann JD, Teriete P, Pickford AR, Campbell ID, Day AJ. The link module from ovulation- and inflammation-associated protein TSG-6 changes conformation on hyaluronan binding. J Biol Chem 2003; 278:49261-70. [PMID: 12972412 DOI: 10.1074/jbc.m309623200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The solution structure of the Link module from human TSG-6, a hyaladherin with important roles in inflammation and ovulation, has been determined in both its free and hyaluronan-bound conformations. This reveals a well defined hyaluronan-binding groove on one face of the Link module that is closed in the absence of ligand. The groove is lined with amino acids that have been implicated in mediating the interaction with hyaluronan, including two tyrosine residues that appear to form essential intermolecular hydrogen bonds and two basic residues capable of supporting ionic interactions. This is the first structure of a non-enzymic hyaladherin in its active state, and identifies a ligand-induced conformational change that is likely to be conserved across the Link module superfamily. NMR and isothermal titration calorimetry experiments with defined oligosaccharides have allowed us to infer the minimum length of hyaluronan that can be accommodated within the binding site and its polarity in the groove; these data have been used to generate a model of the complex formed between the Link module and a hyaluronan octasaccharide.
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Affiliation(s)
- Charles D Blundell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
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